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Fix data region column name references #168

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Merged
labkey-tchad merged 4 commits into from
Jul 2, 2025
Merged

Fix data region column name references #168

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b21ab57
Fix data region column name references
labkey-tchad Jun 30, 2025
5134f64
Fix more column references
labkey-tchad Jul 1, 2025
04d25ad
missed some
labkey-tchad Jul 1, 2025
ade63d1
More fixes
labkey-tchad Jul 1, 2025
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2 changes: 1 addition & 1 deletion OConnorExperiments/test/src/org/labkey/test/tests/OConnorExperimentTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -146,7 +146,7 @@ protected void verifyExperimentWebpart(int row, String description, @Nullable St
assertEquals(description, table.getDataAsText(row, "Description"));
if (type != null)
{
assertEquals(type, table.getDataAsText(row, "ExperimentType"));
assertEquals(type, table.getDataAsText(row, "ExperimentTypeId"));
}

// Make sure each component of the ParentExperiments column is rendered with a link to the begin page for that experiment
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38 changes: 19 additions & 19 deletions genotyping/test/src/org/labkey/test/tests/HaplotypeAssayTest.java
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Expand Up @@ -160,10 +160,10 @@ private void verifyAribitraryHaplotypeAssay()
clickAndWait(Locator.linkWithText(DRB_RUN));
DataRegionTable drt = new DataRegionTable("Data", this);

verifyColumnDataValues(drt, "MHC-AHaplotype1", "A001", "A023", "A001", "A004", "A002a");
verifyColumnDataValues(drt, "MHC-AHaplotype2", "A023", "A021", "A001", "A023", "A002a");
verifyColumnDataValues(drt, "MHC-DRB Haplotype 1", "D025a", "D012b", "D001c", "D012b", "D002");
verifyColumnDataValues(drt, "MHC-DRB Haplotype 2", "D015c", "D017a", "D017a", "D012b", "D002");
verifyColumnDataValues(drt, "mhcAHaplotype1", "A001", "A023", "A001", "A004", "A002a");
verifyColumnDataValues(drt, "mhcAHaplotype2", "A023", "A021", "A001", "A023", "A002a");
verifyColumnDataValues(drt, "mhcDRBHaplotype1", "D025a", "D012b", "D001c", "D012b", "D002");
verifyColumnDataValues(drt, "mhcDRBHaplotype2", "D015c", "D017a", "D017a", "D012b", "D002");

importRun(STR_RUN, DRB_ASSAY, STR_RUN_FILE, true);

Expand Down Expand Up @@ -286,13 +286,13 @@ private void verifyFirstRun()
verifyColumnDataValues(drt, "Animal", "ID-1", "ID-2", "ID-3", "ID-4", "ID-5");
verifyColumnDataValues(drt, "TotalReads", "1000", "2000", "3000", "4000", "5000");
verifyColumnDataValues(drt, "IdentifiedReads", "300", "1000", "600", "2500", "3250");
verifyColumnDataValues(drt, "%Unknown", "70.0", "50.0", "80.0", "37.5", "35.0");
verifyColumnDataValues(drt, "MHC-AHaplotype1", "A001", "A023", "A001", "A004", "A002a");
verifyColumnDataValues(drt, "MHC-AHaplotype2", "A023", "A021", "A001", "A023", "A002a");
verifyColumnDataValues(drt, "MHC-BHaplotype1", "B015c", "B012b", "B001c", "B012b", "B002");
verifyColumnDataValues(drt, "MHC-BHaplotype2", "B025a", "B017a", "B017a", "B012b", "B002");
verifyColumnDataValues(drt, "PercentUnknown", "70.0", "50.0", "80.0", "37.5", "35.0");
verifyColumnDataValues(drt, "mhcAHaplotype1", "A001", "A023", "A001", "A004", "A002a");
verifyColumnDataValues(drt, "mhcAHaplotype2", "A023", "A021", "A001", "A023", "A002a");
verifyColumnDataValues(drt, "mhcBHaplotype1", "B015c", "B012b", "B001c", "B012b", "B002");
verifyColumnDataValues(drt, "mhcBHaplotype2", "B025a", "B017a", "B017a", "B012b", "B002");
verifyColumnDataValues(drt, "Enabled", "true", "true", "true", "true", "true");
verifyColumnDataValues(drt, "ClientAnimalId", "x123", "x234", "x345", "x456", "x567");
verifyColumnDataValues(drt, "AnimalId/ClientAnimalId", "x123", "x234", "x345", "x456", "x567");

// verify concatenated haplotype strings
List<String> concatenated = drt.getColumnDataAsText("ConcatenatedHaplotypes");
Expand All @@ -307,8 +307,8 @@ private void verifyFirstRun()
goToQuery("Animal");
drt = new DataRegionTable("query", this);
assertEquals("Unexpected number of Animal records", 5, drt.getDataRowCount());
verifyColumnDataValues(drt, "Lab Animal Id", "ID-1", "ID-2", "ID-3", "ID-4", "ID-5");
verifyColumnDataValues(drt, "Client Animal Id", "x123", "x234", "x345", "x456", "x567");
verifyColumnDataValues(drt, "LabAnimalId", "ID-1", "ID-2", "ID-3", "ID-4", "ID-5");
verifyColumnDataValues(drt, "ClientAnimalId", "x123", "x234", "x345", "x456", "x567");

verifyHaplotypeRecordsByType(11, 5, 6);
}
Expand Down Expand Up @@ -344,7 +344,7 @@ private void verifySecondRun(String prefix)
verifyColumnDataValues(drt, "Animal", "ID-4", "ID-5", "ID-6", "ID-7", "ID-8", "ID-9");
verifyColumnDataValues(drt, "TotalReads", "4000", "5000", "6000", "7000", " ", "0");
verifyColumnDataValues(drt, "IdentifiedReads", "2500", "3250", "3000", "3500", " ", "1");
verifyColumnDataValues(drt, "%Unknown", "37.5", "35.0", "50.0", "50.0", " ", " ");
verifyColumnDataValues(drt, "PercentUnknown", "37.5", "35.0", "50.0", "50.0", " ", " ");
verifyColumnDataValues(drt, prefix+"-AHaplotype1", "A001", " ", "A033", "A004", "A004", "A004");
verifyColumnDataValues(drt, prefix+"-AHaplotype2", "A023", " ", "A033", " ", "A004", "A004");
verifyColumnDataValues(drt, prefix+"-BHaplotype1", "B015c", " ", "B012b", "B033", "B033", "B033");
Expand Down Expand Up @@ -398,14 +398,14 @@ private void verifyExtraHaplotypeAssignment()
waitForElement(Locator.paginationText(1, 39, 39));

// ADD: animal ID-5, haplotype A001
DataRegionTable.findDataRegion(this).clickInsertNewRow();
DataRegionTable.DataRegion(getDriver()).find().clickInsertNewRow();
selectOptionByText(Locator.name("quf_HaplotypeId"), "A001");
selectOptionByText(Locator.name("quf_AnimalAnalysisId"), animalAnalysisId);
setFormElement(Locator.name("quf_DiploidNumber"), "1");
clickButton("Submit");

// ADD: animal ID-5, haplotype B002
DataRegionTable.findDataRegion(this).clickInsertNewRow();
DataRegionTable.DataRegion(getDriver()).find().clickInsertNewRow();
selectOptionByText(Locator.name("quf_HaplotypeId"), "B002");
selectOptionByText(Locator.name("quf_AnimalAnalysisId"), animalAnalysisId);
setFormElement(Locator.name("quf_DiploidNumber"), "1");
Expand All @@ -416,10 +416,10 @@ private void verifyExtraHaplotypeAssignment()
goToAssayRun("first run");
drt = new DataRegionTable("Data", this);
drt.setFilter("AnimalId", "Equals", "ID-5");
verifyColumnDataValues(drt, "MHC-AHaplotype1", "A001");
verifyColumnDataValues(drt, "MHC-AHaplotype2", "A002a");
verifyColumnDataValues(drt, "MHC-BHaplotype1", "B002");
verifyColumnDataValues(drt, "MHC-BHaplotype2", "B002");
verifyColumnDataValues(drt, "mhcAHaplotype1", "A001");
verifyColumnDataValues(drt, "mhcAHaplotype2", "A002a");
verifyColumnDataValues(drt, "mhcBHaplotype1", "B002");
verifyColumnDataValues(drt, "mhcBHaplotype2", "B002");
drt.clearFilter("AnimalId");

// NOTE: this should clean up what it has done in order to make the test more modular...
Expand Down